Starting phenix.real_space_refine on Thu Mar 5 19:55:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ul7_26594/03_2026/7ul7_26594.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ul7_26594/03_2026/7ul7_26594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ul7_26594/03_2026/7ul7_26594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ul7_26594/03_2026/7ul7_26594.map" model { file = "/net/cci-nas-00/data/ceres_data/7ul7_26594/03_2026/7ul7_26594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ul7_26594/03_2026/7ul7_26594.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9444 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 10986 2.51 5 N 2922 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17439 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain breaks: 2 Chain: "D" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1579 Classifications: {'peptide': 205} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "E" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1621 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Chain: "A" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain breaks: 2 Chain: "L" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1579 Classifications: {'peptide': 205} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "H" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1621 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Chain: "B" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain breaks: 2 Chain: "F" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1579 Classifications: {'peptide': 205} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "G" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1621 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Chain: "c" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1225 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "b" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1225 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "a" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1225 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.33, per 1000 atoms: 0.25 Number of scatterers: 17439 At special positions: 0 Unit cell: (187.92, 178.848, 103.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 3420 8.00 N 2922 7.00 C 10986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 206 " distance=2.03 Simple disulfide: pdb=" SG CYS c 278 " - pdb=" SG CYS c 291 " distance=2.03 Simple disulfide: pdb=" SG CYS c 300 " - pdb=" SG CYS c 309 " distance=2.03 Simple disulfide: pdb=" SG CYS c 363 " - pdb=" SG CYS c 384 " distance=2.03 Simple disulfide: pdb=" SG CYS b 278 " - pdb=" SG CYS b 291 " distance=2.03 Simple disulfide: pdb=" SG CYS b 300 " - pdb=" SG CYS b 309 " distance=2.03 Simple disulfide: pdb=" SG CYS b 363 " - pdb=" SG CYS b 384 " distance=2.02 Simple disulfide: pdb=" SG CYS a 278 " - pdb=" SG CYS a 291 " distance=2.03 Simple disulfide: pdb=" SG CYS a 300 " - pdb=" SG CYS a 309 " distance=2.03 Simple disulfide: pdb=" SG CYS a 363 " - pdb=" SG CYS a 384 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 301 " - " ASN A 88 " " NAG A 302 " - " ASN A 108 " " NAG A 303 " - " ASN A 166 " " NAG A 304 " - " ASN A 223 " " NAG A 305 " - " ASN A 118 " " NAG B 301 " - " ASN B 108 " " NAG B 302 " - " ASN B 166 " " NAG B 303 " - " ASN B 223 " " NAG C 301 " - " ASN C 88 " " NAG C 302 " - " ASN C 108 " " NAG C 303 " - " ASN C 166 " " NAG C 304 " - " ASN C 223 " " NAG C 305 " - " ASN C 118 " " NAG I 1 " - " ASN C 78 " " NAG J 1 " - " ASN A 78 " " NAG K 1 " - " ASN B 78 " " NAG M 1 " - " ASN B 88 " " NAG a 501 " - " ASN a 389 " " NAG a 502 " - " ASN a 372 " " NAG a 503 " - " ASN a 394 " " NAG b 501 " - " ASN b 372 " " NAG b 502 " - " ASN b 389 " " NAG b 503 " - " ASN b 394 " " NAG c 501 " - " ASN c 372 " " NAG c 502 " - " ASN c 389 " " NAG c 503 " - " ASN c 394 " Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 779.2 milliseconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4068 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 37 sheets defined 19.5% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'C' and resid 119 through 125 Processing helix chain 'C' and resid 132 through 143 removed outlier: 4.041A pdb=" N ILE C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE C 143 " --> pdb=" O PHE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.505A pdb=" N LYS C 160 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.594A pdb=" N GLY C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 removed outlier: 3.709A pdb=" N SER D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY D 130 " --> pdb=" O GLN D 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 125 through 130' Processing helix chain 'D' and resid 185 through 189 Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 211 through 214 Processing helix chain 'A' and resid 119 through 126 removed outlier: 4.167A pdb=" N ASN A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 removed outlier: 4.204A pdb=" N ILE A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.675A pdb=" N LEU A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 242' Processing helix chain 'L' and resid 124 through 128 Processing helix chain 'L' and resid 186 through 190 removed outlier: 3.871A pdb=" N LYS L 190 " --> pdb=" O ASP L 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'H' and resid 211 through 214 Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.633A pdb=" N HIS B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 removed outlier: 3.925A pdb=" N ILE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 143 " --> pdb=" O PHE B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.673A pdb=" N LEU B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 124 through 129 removed outlier: 3.815A pdb=" N LEU F 127 " --> pdb=" O ASP F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 removed outlier: 4.051A pdb=" N GLU F 189 " --> pdb=" O LYS F 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 185 through 189' Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 197 through 199 No H-bonds generated for 'chain 'G' and resid 197 through 199' Processing helix chain 'G' and resid 212 through 214 No H-bonds generated for 'chain 'G' and resid 212 through 214' Processing helix chain 'c' and resid 293 through 298 Processing helix chain 'c' and resid 299 through 303 removed outlier: 3.621A pdb=" N LYS c 303 " --> pdb=" O CYS c 300 " (cutoff:3.500A) Processing helix chain 'c' and resid 308 through 324 removed outlier: 3.824A pdb=" N ARG c 323 " --> pdb=" O LYS c 319 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG c 324 " --> pdb=" O GLN c 320 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 344 removed outlier: 5.489A pdb=" N ASN c 341 " --> pdb=" O ASN c 337 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ALA c 342 " --> pdb=" O LYS c 338 " (cutoff:3.500A) Processing helix chain 'c' and resid 345 through 358 removed outlier: 3.987A pdb=" N ILE c 349 " --> pdb=" O ASN c 345 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET c 358 " --> pdb=" O LEU c 354 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 397 No H-bonds generated for 'chain 'c' and resid 395 through 397' Processing helix chain 'c' and resid 398 through 414 removed outlier: 3.964A pdb=" N ALA c 406 " --> pdb=" O ILE c 402 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN c 408 " --> pdb=" O GLN c 404 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU c 414 " --> pdb=" O ILE c 410 " (cutoff:3.500A) Processing helix chain 'b' and resid 293 through 298 Processing helix chain 'b' and resid 299 through 303 removed outlier: 3.714A pdb=" N GLU b 302 " --> pdb=" O LYS b 299 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS b 303 " --> pdb=" O CYS b 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 299 through 303' Processing helix chain 'b' and resid 307 through 325 removed outlier: 3.525A pdb=" N MET b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG b 323 " --> pdb=" O LYS b 319 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU b 325 " --> pdb=" O ALA b 321 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 338 Processing helix chain 'b' and resid 339 through 344 removed outlier: 3.708A pdb=" N LEU b 343 " --> pdb=" O ALA b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 345 through 358 removed outlier: 4.153A pdb=" N ILE b 349 " --> pdb=" O ASN b 345 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 397 No H-bonds generated for 'chain 'b' and resid 395 through 397' Processing helix chain 'b' and resid 398 through 414 removed outlier: 3.892A pdb=" N ALA b 406 " --> pdb=" O ILE b 402 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN b 408 " --> pdb=" O GLN b 404 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE b 410 " --> pdb=" O ALA b 406 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU b 414 " --> pdb=" O ILE b 410 " (cutoff:3.500A) Processing helix chain 'a' and resid 280 through 284 removed outlier: 3.600A pdb=" N LEU a 284 " --> pdb=" O ARG a 281 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 298 Processing helix chain 'a' and resid 299 through 303 removed outlier: 3.589A pdb=" N GLU a 302 " --> pdb=" O LYS a 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS a 303 " --> pdb=" O CYS a 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 299 through 303' Processing helix chain 'a' and resid 307 through 325 removed outlier: 3.542A pdb=" N LEU a 325 " --> pdb=" O ALA a 321 " (cutoff:3.500A) Processing helix chain 'a' and resid 333 through 344 removed outlier: 6.095A pdb=" N ASN a 341 " --> pdb=" O ASN a 337 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA a 342 " --> pdb=" O LYS a 338 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 358 removed outlier: 4.003A pdb=" N ILE a 349 " --> pdb=" O ASN a 345 " (cutoff:3.500A) Processing helix chain 'a' and resid 394 through 397 Processing helix chain 'a' and resid 398 through 413 removed outlier: 4.001A pdb=" N ALA a 406 " --> pdb=" O ILE a 402 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN a 408 " --> pdb=" O GLN a 404 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET a 409 " --> pdb=" O GLN a 405 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE a 410 " --> pdb=" O ALA a 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 66 through 71 removed outlier: 3.740A pdb=" N LYS c 383 " --> pdb=" O TRP c 369 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 88 removed outlier: 3.550A pdb=" N CYS C 85 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS C 87 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N HIS C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY C 101 " --> pdb=" O THR C 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 5 through 7 removed outlier: 4.064A pdb=" N CYS D 23 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE D 72 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.490A pdb=" N LEU D 11 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 104 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.490A pdb=" N LEU D 11 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 104 " --> pdb=" O TYR D 87 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 116 through 120 removed outlier: 6.120A pdb=" N TYR D 175 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 147 through 151 Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 removed outlier: 4.470A pdb=" N GLN E 3 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.861A pdb=" N GLY E 10 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR E 60 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 130 through 134 removed outlier: 3.806A pdb=" N ASP E 154 " --> pdb=" O TYR E 186 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR E 186 " --> pdb=" O ASP E 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 161 through 164 Processing sheet with id=AB3, first strand: chain 'A' and resid 67 through 71 Processing sheet with id=AB4, first strand: chain 'A' and resid 83 through 88 removed outlier: 5.619A pdb=" N SER A 84 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ARG A 95 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR A 86 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR A 93 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN A 88 " --> pdb=" O HIS A 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.936A pdb=" N CYS L 23 " --> pdb=" O PHE L 72 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE L 72 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.558A pdb=" N LEU L 11 " --> pdb=" O GLU L 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.686A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 116 through 120 removed outlier: 6.233A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 147 through 151 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.254A pdb=" N GLN H 3 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.592A pdb=" N GLY H 10 " --> pdb=" O ILE H 120 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.958A pdb=" N ASP H 154 " --> pdb=" O TYR H 186 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 161 through 164 Processing sheet with id=AC5, first strand: chain 'B' and resid 66 through 71 removed outlier: 4.410A pdb=" N ASN b 364 " --> pdb=" O TRP b 385 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TRP b 385 " --> pdb=" O ASN b 364 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N SER b 366 " --> pdb=" O LYS b 383 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N LYS b 383 " --> pdb=" O SER b 366 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.722A pdb=" N VAL B 163 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AC8, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.450A pdb=" N LEU F 11 " --> pdb=" O GLU F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 46 through 50 removed outlier: 5.508A pdb=" N LEU F 47 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR F 91 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 116 through 120 removed outlier: 6.058A pdb=" N TYR F 175 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 146 through 152 removed outlier: 3.979A pdb=" N VAL F 207 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N HIS F 200 " --> pdb=" O SER F 205 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N SER F 205 " --> pdb=" O HIS F 200 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 6 through 8 removed outlier: 3.841A pdb=" N SER G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.921A pdb=" N GLY G 10 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N MET G 34 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR G 60 " --> pdb=" O SER G 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 130 through 134 removed outlier: 4.858A pdb=" N ALA G 147 " --> pdb=" O VAL G 194 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL G 194 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLY G 149 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL G 192 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU G 151 " --> pdb=" O SER G 190 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER G 190 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS G 153 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU G 188 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 160 through 164 Processing sheet with id=AD7, first strand: chain 'c' and resid 278 through 279 Processing sheet with id=AD8, first strand: chain 'c' and resid 387 through 388 Processing sheet with id=AD9, first strand: chain 'b' and resid 278 through 279 Processing sheet with id=AE1, first strand: chain 'a' and resid 278 through 279 594 hydrogen bonds defined for protein. 1521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5517 1.35 - 1.47: 4696 1.47 - 1.59: 7445 1.59 - 1.72: 0 1.72 - 1.84: 162 Bond restraints: 17820 Sorted by residual: bond pdb=" C1 NAG a 503 " pdb=" O5 NAG a 503 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" CB PRO D 206 " pdb=" CG PRO D 206 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.57e+00 bond pdb=" CB PRO E 133 " pdb=" CG PRO E 133 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.86e+00 bond pdb=" C1 NAG A 304 " pdb=" O5 NAG A 304 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" C1 NAG B 303 " pdb=" O5 NAG B 303 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 17815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 23787 2.37 - 4.73: 340 4.73 - 7.10: 29 7.10 - 9.46: 3 9.46 - 11.83: 3 Bond angle restraints: 24162 Sorted by residual: angle pdb=" CA PRO D 206 " pdb=" N PRO D 206 " pdb=" CD PRO D 206 " ideal model delta sigma weight residual 112.00 105.30 6.70 1.40e+00 5.10e-01 2.29e+01 angle pdb=" CB MET C 133 " pdb=" CG MET C 133 " pdb=" SD MET C 133 " ideal model delta sigma weight residual 112.70 124.53 -11.83 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CA CYS A 154 " pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " ideal model delta sigma weight residual 114.40 122.52 -8.12 2.30e+00 1.89e-01 1.24e+01 angle pdb=" CA GLU C 227 " pdb=" CB GLU C 227 " pdb=" CG GLU C 227 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CB LYS B 87 " pdb=" CG LYS B 87 " pdb=" CD LYS B 87 " ideal model delta sigma weight residual 111.30 117.93 -6.63 2.30e+00 1.89e-01 8.30e+00 ... (remaining 24157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 9754 16.14 - 32.27: 946 32.27 - 48.41: 254 48.41 - 64.55: 68 64.55 - 80.69: 18 Dihedral angle restraints: 11040 sinusoidal: 4716 harmonic: 6324 Sorted by residual: dihedral pdb=" CB CYS b 363 " pdb=" SG CYS b 363 " pdb=" SG CYS b 384 " pdb=" CB CYS b 384 " ideal model delta sinusoidal sigma weight residual -86.00 -147.60 61.60 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS a 363 " pdb=" SG CYS a 363 " pdb=" SG CYS a 384 " pdb=" CB CYS a 384 " ideal model delta sinusoidal sigma weight residual -86.00 -145.77 59.77 1 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" CB CYS b 278 " pdb=" SG CYS b 278 " pdb=" SG CYS b 291 " pdb=" CB CYS b 291 " ideal model delta sinusoidal sigma weight residual -86.00 -27.29 -58.71 1 1.00e+01 1.00e-02 4.61e+01 ... (remaining 11037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2628 0.097 - 0.193: 143 0.193 - 0.290: 6 0.290 - 0.386: 3 0.386 - 0.483: 1 Chirality restraints: 2781 Sorted by residual: chirality pdb=" C1 NAG a 503 " pdb=" ND2 ASN a 394 " pdb=" C2 NAG a 503 " pdb=" O5 NAG a 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C 78 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 78 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 2778 not shown) Planarity restraints: 3047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 385 " 0.029 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP a 385 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP a 385 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP a 385 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP a 385 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 385 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP a 385 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP b 385 " 0.026 2.00e-02 2.50e+03 2.38e-02 1.41e+01 pdb=" CG TRP b 385 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP b 385 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP b 385 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP b 385 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP b 385 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP b 385 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 385 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 385 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP b 385 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 59 " -0.054 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO F 60 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO F 60 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 60 " -0.045 5.00e-02 4.00e+02 ... (remaining 3044 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 711 2.71 - 3.26: 17124 3.26 - 3.81: 26466 3.81 - 4.35: 31822 4.35 - 4.90: 54359 Nonbonded interactions: 130482 Sorted by model distance: nonbonded pdb=" OD1 ASP G 111 " pdb=" N VAL G 112 " model vdw 2.165 3.120 nonbonded pdb=" OD1 ASP E 111 " pdb=" N VAL E 112 " model vdw 2.180 3.120 nonbonded pdb=" O ASN C 184 " pdb=" NE2 GLN C 188 " model vdw 2.198 3.120 nonbonded pdb=" OG SER c 332 " pdb=" OE1 GLN c 334 " model vdw 2.205 3.040 nonbonded pdb=" O LEU L 127 " pdb=" NZ LYS L 185 " model vdw 2.210 3.120 ... (remaining 130477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 65 through 303) selection = chain 'B' selection = (chain 'C' and resid 65 through 303) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.960 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 17877 Z= 0.200 Angle : 0.735 20.954 24306 Z= 0.358 Chirality : 0.049 0.483 2781 Planarity : 0.005 0.083 3021 Dihedral : 13.880 80.686 6891 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.18), residues: 2124 helix: -1.18 (0.29), residues: 288 sheet: 0.36 (0.21), residues: 663 loop : -1.13 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 88 TYR 0.017 0.002 TYR G 155 PHE 0.036 0.002 PHE b 308 TRP 0.065 0.002 TRP a 385 HIS 0.011 0.001 HIS G 210 Details of bonding type rmsd covalent geometry : bond 0.00458 (17820) covalent geometry : angle 0.68492 (24162) SS BOND : bond 0.00450 ( 27) SS BOND : angle 2.05153 ( 54) hydrogen bonds : bond 0.15785 ( 593) hydrogen bonds : angle 7.31152 ( 1521) link_BETA1-4 : bond 0.00092 ( 4) link_BETA1-4 : angle 2.47075 ( 12) link_NAG-ASN : bond 0.01121 ( 26) link_NAG-ASN : angle 4.39721 ( 78) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7656 (t0) cc_final: 0.7438 (t0) REVERT: C 102 LEU cc_start: 0.7200 (mm) cc_final: 0.6989 (mp) REVERT: D 83 ASP cc_start: 0.7091 (m-30) cc_final: 0.6829 (m-30) REVERT: E 179 VAL cc_start: 0.8336 (p) cc_final: 0.8022 (m) REVERT: A 66 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6467 (tm-30) REVERT: A 103 GLU cc_start: 0.6635 (tt0) cc_final: 0.6375 (tt0) REVERT: A 221 ILE cc_start: 0.7135 (mp) cc_final: 0.6896 (mp) REVERT: L 174 THR cc_start: 0.7925 (m) cc_final: 0.7680 (m) REVERT: H 126 THR cc_start: 0.8315 (t) cc_final: 0.8103 (m) REVERT: H 211 LYS cc_start: 0.8289 (tppt) cc_final: 0.7898 (tppt) REVERT: B 87 LYS cc_start: 0.7058 (tppt) cc_final: 0.6551 (tppt) REVERT: c 383 LYS cc_start: 0.7574 (ptpp) cc_final: 0.7350 (ptpp) REVERT: b 383 LYS cc_start: 0.7203 (ptpp) cc_final: 0.6968 (ptpp) REVERT: a 283 MET cc_start: 0.6656 (tpt) cc_final: 0.6268 (mmm) REVERT: a 356 ASP cc_start: 0.7187 (t70) cc_final: 0.6953 (t0) REVERT: a 392 TYR cc_start: 0.6966 (m-80) cc_final: 0.6593 (m-80) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.1309 time to fit residues: 89.5448 Evaluate side-chains 445 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.0070 chunk 212 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 GLN D 90 GLN E 6 GLN ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN A 126 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN G 35 ASN c 373 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.171913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.142481 restraints weight = 29032.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147547 restraints weight = 15801.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.150897 restraints weight = 10385.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.153113 restraints weight = 7732.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.154566 restraints weight = 6274.457| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 17877 Z= 0.164 Angle : 0.720 19.459 24306 Z= 0.349 Chirality : 0.046 0.263 2781 Planarity : 0.005 0.072 3021 Dihedral : 7.575 57.151 2973 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.83 % Allowed : 10.41 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.18), residues: 2124 helix: -1.08 (0.29), residues: 312 sheet: 0.54 (0.21), residues: 642 loop : -1.00 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 355 TYR 0.027 0.002 TYR D 50 PHE 0.025 0.002 PHE a 261 TRP 0.028 0.002 TRP a 385 HIS 0.010 0.001 HIS G 210 Details of bonding type rmsd covalent geometry : bond 0.00377 (17820) covalent geometry : angle 0.67214 (24162) SS BOND : bond 0.00527 ( 27) SS BOND : angle 1.70652 ( 54) hydrogen bonds : bond 0.04939 ( 593) hydrogen bonds : angle 6.41769 ( 1521) link_BETA1-4 : bond 0.00251 ( 4) link_BETA1-4 : angle 1.74832 ( 12) link_NAG-ASN : bond 0.00784 ( 26) link_NAG-ASN : angle 4.34617 ( 78) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 450 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7563 (mmm) cc_final: 0.6701 (tpt) REVERT: C 195 TRP cc_start: 0.7181 (t60) cc_final: 0.6929 (t60) REVERT: D 83 ASP cc_start: 0.7277 (m-30) cc_final: 0.6738 (m-30) REVERT: D 107 GLU cc_start: 0.6512 (pt0) cc_final: 0.6044 (pt0) REVERT: E 83 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7580 (tp-100) REVERT: E 179 VAL cc_start: 0.8368 (p) cc_final: 0.8049 (m) REVERT: A 66 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6469 (tm-30) REVERT: A 103 GLU cc_start: 0.6660 (tt0) cc_final: 0.6381 (tt0) REVERT: L 82 GLU cc_start: 0.7074 (mp0) cc_final: 0.6747 (mp0) REVERT: H 88 ARG cc_start: 0.7228 (mmm160) cc_final: 0.6771 (mmm160) REVERT: H 126 THR cc_start: 0.8298 (t) cc_final: 0.8079 (m) REVERT: H 211 LYS cc_start: 0.8280 (tppt) cc_final: 0.7892 (tppt) REVERT: B 81 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6718 (mtm) REVERT: B 87 LYS cc_start: 0.7083 (tppt) cc_final: 0.6780 (tppt) REVERT: B 88 ASN cc_start: 0.7638 (p0) cc_final: 0.7436 (p0) REVERT: B 133 MET cc_start: 0.7729 (mmm) cc_final: 0.7508 (tpt) REVERT: B 165 TYR cc_start: 0.7598 (m-80) cc_final: 0.7392 (m-10) REVERT: B 236 SER cc_start: 0.7344 (t) cc_final: 0.7121 (m) REVERT: F 6 GLN cc_start: 0.6718 (mp10) cc_final: 0.6463 (mp10) REVERT: F 38 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8074 (tp40) REVERT: G 118 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7699 (p) REVERT: b 320 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.6631 (mp10) REVERT: a 283 MET cc_start: 0.6213 (tpt) cc_final: 0.5999 (mmm) REVERT: a 356 ASP cc_start: 0.7197 (t70) cc_final: 0.6836 (t0) REVERT: a 367 LYS cc_start: 0.7895 (ptmt) cc_final: 0.7643 (ptmt) REVERT: a 392 TYR cc_start: 0.7041 (m-80) cc_final: 0.6681 (m-80) outliers start: 35 outliers final: 20 residues processed: 461 average time/residue: 0.1380 time to fit residues: 95.8726 Evaluate side-chains 458 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 434 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain a residue 295 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 123 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 158 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 102 HIS ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 HIS ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS c 408 ASN a 352 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.170547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141667 restraints weight = 29308.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.146400 restraints weight = 16527.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.149520 restraints weight = 11154.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.151686 restraints weight = 8453.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.153150 restraints weight = 6915.622| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17877 Z= 0.199 Angle : 0.709 19.113 24306 Z= 0.343 Chirality : 0.045 0.293 2781 Planarity : 0.005 0.066 3021 Dihedral : 7.322 59.100 2973 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.51 % Allowed : 13.76 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.18), residues: 2124 helix: -1.17 (0.28), residues: 312 sheet: 0.40 (0.21), residues: 672 loop : -1.04 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 99 TYR 0.025 0.002 TYR D 50 PHE 0.019 0.002 PHE a 261 TRP 0.028 0.002 TRP a 385 HIS 0.009 0.001 HIS G 210 Details of bonding type rmsd covalent geometry : bond 0.00459 (17820) covalent geometry : angle 0.66227 (24162) SS BOND : bond 0.00525 ( 27) SS BOND : angle 1.55836 ( 54) hydrogen bonds : bond 0.04776 ( 593) hydrogen bonds : angle 6.27188 ( 1521) link_BETA1-4 : bond 0.00346 ( 4) link_BETA1-4 : angle 1.89875 ( 12) link_NAG-ASN : bond 0.00786 ( 26) link_NAG-ASN : angle 4.30016 ( 78) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 437 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 LYS cc_start: 0.6927 (mmmt) cc_final: 0.6620 (tppt) REVERT: C 133 MET cc_start: 0.7609 (mmm) cc_final: 0.7277 (mmm) REVERT: C 154 CYS cc_start: 0.2953 (OUTLIER) cc_final: 0.2578 (p) REVERT: D 83 ASP cc_start: 0.7388 (m-30) cc_final: 0.7035 (m-30) REVERT: D 107 GLU cc_start: 0.6404 (pt0) cc_final: 0.5964 (pt0) REVERT: E 30 LYS cc_start: 0.7774 (ptmt) cc_final: 0.7325 (ptmm) REVERT: E 83 GLN cc_start: 0.7819 (tp-100) cc_final: 0.7604 (tp-100) REVERT: E 179 VAL cc_start: 0.8345 (p) cc_final: 0.8047 (m) REVERT: A 66 GLU cc_start: 0.6913 (tm-30) cc_final: 0.6523 (tm-30) REVERT: A 103 GLU cc_start: 0.6610 (tt0) cc_final: 0.6336 (tt0) REVERT: A 213 MET cc_start: 0.6989 (tmm) cc_final: 0.6770 (tmm) REVERT: H 54 ARG cc_start: 0.7738 (ptt180) cc_final: 0.7483 (ptp-170) REVERT: H 88 ARG cc_start: 0.7142 (mmm160) cc_final: 0.6777 (mmm160) REVERT: H 211 LYS cc_start: 0.8281 (tppt) cc_final: 0.7870 (tppt) REVERT: B 236 SER cc_start: 0.7504 (t) cc_final: 0.7276 (m) REVERT: F 6 GLN cc_start: 0.6814 (mp10) cc_final: 0.6508 (mp10) REVERT: G 118 THR cc_start: 0.7948 (p) cc_final: 0.7685 (p) REVERT: G 153 LYS cc_start: 0.7282 (ttmm) cc_final: 0.7024 (ttmm) REVERT: b 307 GLU cc_start: 0.7703 (tp30) cc_final: 0.7371 (tp30) REVERT: b 320 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6909 (mp10) REVERT: a 356 ASP cc_start: 0.7224 (t70) cc_final: 0.6880 (t0) REVERT: a 392 TYR cc_start: 0.7028 (m-80) cc_final: 0.6767 (m-80) REVERT: a 409 MET cc_start: 0.6320 (mtt) cc_final: 0.6115 (mtt) outliers start: 48 outliers final: 32 residues processed: 451 average time/residue: 0.1249 time to fit residues: 84.0370 Evaluate side-chains 466 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 432 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 30 optimal weight: 0.0050 chunk 159 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 190 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 HIS E 6 GLN E 102 HIS A 126 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS G 3 GLN c 373 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.169995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140322 restraints weight = 29221.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.145401 restraints weight = 15811.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.148747 restraints weight = 10408.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.150880 restraints weight = 7744.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.152493 restraints weight = 6324.916| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17877 Z= 0.212 Angle : 0.720 18.684 24306 Z= 0.348 Chirality : 0.046 0.302 2781 Planarity : 0.005 0.064 3021 Dihedral : 7.043 58.400 2973 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.45 % Allowed : 15.70 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.18), residues: 2124 helix: -1.25 (0.28), residues: 312 sheet: 0.30 (0.21), residues: 678 loop : -1.06 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 99 TYR 0.025 0.002 TYR D 50 PHE 0.031 0.002 PHE a 261 TRP 0.027 0.002 TRP a 385 HIS 0.008 0.001 HIS G 210 Details of bonding type rmsd covalent geometry : bond 0.00487 (17820) covalent geometry : angle 0.67495 (24162) SS BOND : bond 0.00528 ( 27) SS BOND : angle 1.47274 ( 54) hydrogen bonds : bond 0.04637 ( 593) hydrogen bonds : angle 6.24893 ( 1521) link_BETA1-4 : bond 0.00320 ( 4) link_BETA1-4 : angle 1.92825 ( 12) link_NAG-ASN : bond 0.00746 ( 26) link_NAG-ASN : angle 4.26118 ( 78) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 436 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7763 (mmm) cc_final: 0.7370 (mmm) REVERT: C 154 CYS cc_start: 0.3064 (OUTLIER) cc_final: 0.2640 (p) REVERT: D 83 ASP cc_start: 0.7399 (m-30) cc_final: 0.6937 (m-30) REVERT: D 107 GLU cc_start: 0.6640 (pt0) cc_final: 0.6121 (pt0) REVERT: E 30 LYS cc_start: 0.7843 (ptmt) cc_final: 0.7342 (ptmm) REVERT: E 80 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.5985 (pt) REVERT: E 83 GLN cc_start: 0.7963 (tp-100) cc_final: 0.7658 (tp-100) REVERT: E 179 VAL cc_start: 0.8350 (p) cc_final: 0.8030 (m) REVERT: A 66 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6542 (tm-30) REVERT: A 103 GLU cc_start: 0.6712 (tt0) cc_final: 0.6439 (tt0) REVERT: A 213 MET cc_start: 0.7119 (tmm) cc_final: 0.6780 (tmm) REVERT: L 46 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7919 (mtp85) REVERT: H 88 ARG cc_start: 0.7231 (mmm160) cc_final: 0.6881 (mmm160) REVERT: H 99 ARG cc_start: 0.8253 (ttp-170) cc_final: 0.8016 (ttp-170) REVERT: H 126 THR cc_start: 0.8285 (t) cc_final: 0.8071 (m) REVERT: H 211 LYS cc_start: 0.8321 (tppt) cc_final: 0.7896 (tppt) REVERT: B 236 SER cc_start: 0.7502 (t) cc_final: 0.7274 (m) REVERT: G 2 VAL cc_start: 0.8109 (p) cc_final: 0.7813 (p) REVERT: G 118 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7753 (p) REVERT: c 299 LYS cc_start: 0.7576 (mtmm) cc_final: 0.7285 (mtmm) REVERT: b 307 GLU cc_start: 0.7765 (tp30) cc_final: 0.7379 (tp30) REVERT: b 320 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6901 (mp10) REVERT: b 334 GLN cc_start: 0.7259 (mp10) cc_final: 0.7058 (mp10) REVERT: a 356 ASP cc_start: 0.7231 (t70) cc_final: 0.6826 (t0) REVERT: a 392 TYR cc_start: 0.7141 (m-80) cc_final: 0.6900 (m-80) REVERT: a 409 MET cc_start: 0.6466 (mtt) cc_final: 0.6265 (mtt) outliers start: 66 outliers final: 47 residues processed: 458 average time/residue: 0.1383 time to fit residues: 95.2961 Evaluate side-chains 479 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 428 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 336 ILE Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 336 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 6 optimal weight: 0.2980 chunk 141 optimal weight: 0.5980 chunk 208 optimal weight: 0.3980 chunk 83 optimal weight: 0.0470 chunk 67 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 131 optimal weight: 0.0270 chunk 90 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 102 HIS A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 229 HIS c 373 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.171462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.142814 restraints weight = 29036.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.147553 restraints weight = 16356.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.150692 restraints weight = 11006.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.152851 restraints weight = 8325.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.154248 restraints weight = 6808.160| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17877 Z= 0.133 Angle : 0.677 18.594 24306 Z= 0.324 Chirality : 0.044 0.274 2781 Planarity : 0.005 0.061 3021 Dihedral : 6.625 56.033 2973 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.14 % Allowed : 17.01 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.18), residues: 2124 helix: -0.95 (0.30), residues: 294 sheet: 0.28 (0.21), residues: 684 loop : -1.02 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 99 TYR 0.027 0.001 TYR a 365 PHE 0.024 0.001 PHE a 261 TRP 0.022 0.001 TRP C 226 HIS 0.006 0.001 HIS G 210 Details of bonding type rmsd covalent geometry : bond 0.00304 (17820) covalent geometry : angle 0.63105 (24162) SS BOND : bond 0.00421 ( 27) SS BOND : angle 1.30892 ( 54) hydrogen bonds : bond 0.04004 ( 593) hydrogen bonds : angle 6.02469 ( 1521) link_BETA1-4 : bond 0.00353 ( 4) link_BETA1-4 : angle 1.80578 ( 12) link_NAG-ASN : bond 0.00803 ( 26) link_NAG-ASN : angle 4.19714 ( 78) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 432 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7661 (mmm) cc_final: 0.7429 (mmm) REVERT: C 154 CYS cc_start: 0.2922 (OUTLIER) cc_final: 0.2526 (p) REVERT: D 83 ASP cc_start: 0.7392 (m-30) cc_final: 0.7046 (m-30) REVERT: D 107 GLU cc_start: 0.6546 (pt0) cc_final: 0.6096 (pt0) REVERT: E 18 LEU cc_start: 0.7222 (tp) cc_final: 0.7000 (tp) REVERT: E 80 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5959 (pt) REVERT: E 83 GLN cc_start: 0.7887 (tp-100) cc_final: 0.7628 (tp-100) REVERT: E 179 VAL cc_start: 0.8300 (p) cc_final: 0.7994 (m) REVERT: A 66 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6573 (tm-30) REVERT: A 68 GLN cc_start: 0.7549 (mt0) cc_final: 0.7046 (mt0) REVERT: A 103 GLU cc_start: 0.6536 (tt0) cc_final: 0.6282 (tt0) REVERT: A 213 MET cc_start: 0.7085 (tmm) cc_final: 0.6697 (tmm) REVERT: H 88 ARG cc_start: 0.7137 (mmm160) cc_final: 0.6911 (mmm160) REVERT: H 99 ARG cc_start: 0.8154 (ttp-170) cc_final: 0.7916 (ttp-170) REVERT: H 211 LYS cc_start: 0.8261 (tppt) cc_final: 0.7859 (tppt) REVERT: B 133 MET cc_start: 0.7570 (tpp) cc_final: 0.7154 (tpt) REVERT: B 236 SER cc_start: 0.7657 (t) cc_final: 0.7412 (m) REVERT: G 118 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7639 (p) REVERT: c 299 LYS cc_start: 0.7549 (mtmm) cc_final: 0.7243 (mtmm) REVERT: b 307 GLU cc_start: 0.7741 (tp30) cc_final: 0.7429 (tp30) REVERT: b 320 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.6961 (mp10) REVERT: a 307 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7098 (mm-30) REVERT: a 356 ASP cc_start: 0.7195 (t70) cc_final: 0.6931 (t70) REVERT: a 392 TYR cc_start: 0.7096 (m-80) cc_final: 0.6862 (m-80) outliers start: 60 outliers final: 45 residues processed: 452 average time/residue: 0.1391 time to fit residues: 94.7035 Evaluate side-chains 470 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 421 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 401 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 178 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 193 optimal weight: 0.2980 chunk 192 optimal weight: 0.0000 chunk 204 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 152 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 180 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS A 157 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS c 373 HIS c 408 ASN a 352 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.171041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141379 restraints weight = 29068.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.146219 restraints weight = 15769.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.149684 restraints weight = 10529.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.151835 restraints weight = 7812.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.153525 restraints weight = 6371.966| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17877 Z= 0.150 Angle : 0.677 18.092 24306 Z= 0.324 Chirality : 0.044 0.272 2781 Planarity : 0.004 0.059 3021 Dihedral : 6.407 55.698 2973 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.45 % Allowed : 17.90 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.18), residues: 2124 helix: -0.86 (0.31), residues: 294 sheet: 0.33 (0.21), residues: 684 loop : -1.00 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 313 TYR 0.024 0.001 TYR D 50 PHE 0.021 0.001 PHE a 261 TRP 0.014 0.002 TRP a 385 HIS 0.006 0.001 HIS G 210 Details of bonding type rmsd covalent geometry : bond 0.00347 (17820) covalent geometry : angle 0.63294 (24162) SS BOND : bond 0.00451 ( 27) SS BOND : angle 1.29345 ( 54) hydrogen bonds : bond 0.04002 ( 593) hydrogen bonds : angle 5.94179 ( 1521) link_BETA1-4 : bond 0.00272 ( 4) link_BETA1-4 : angle 1.86768 ( 12) link_NAG-ASN : bond 0.00746 ( 26) link_NAG-ASN : angle 4.10674 ( 78) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 420 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7745 (mmm) cc_final: 0.7412 (mmm) REVERT: C 154 CYS cc_start: 0.3032 (OUTLIER) cc_final: 0.2624 (p) REVERT: D 83 ASP cc_start: 0.7387 (m-30) cc_final: 0.7012 (m-30) REVERT: D 107 GLU cc_start: 0.6589 (pt0) cc_final: 0.6104 (pt0) REVERT: E 80 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5931 (pt) REVERT: E 83 GLN cc_start: 0.7908 (tp-100) cc_final: 0.7638 (tp-100) REVERT: E 179 VAL cc_start: 0.8302 (p) cc_final: 0.7983 (m) REVERT: A 66 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6579 (tm-30) REVERT: A 68 GLN cc_start: 0.7541 (mt0) cc_final: 0.7022 (mt0) REVERT: A 103 GLU cc_start: 0.6596 (tt0) cc_final: 0.6327 (tt0) REVERT: A 213 MET cc_start: 0.7144 (tmm) cc_final: 0.6735 (tmm) REVERT: H 88 ARG cc_start: 0.7177 (mmm160) cc_final: 0.6869 (mmm160) REVERT: H 211 LYS cc_start: 0.8315 (tppt) cc_final: 0.7891 (tppt) REVERT: B 87 LYS cc_start: 0.7110 (tppt) cc_final: 0.6835 (tppt) REVERT: B 133 MET cc_start: 0.7601 (tpp) cc_final: 0.6814 (tpt) REVERT: B 236 SER cc_start: 0.7671 (t) cc_final: 0.7407 (m) REVERT: G 118 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7678 (p) REVERT: c 299 LYS cc_start: 0.7565 (mtmm) cc_final: 0.7265 (mtmm) REVERT: b 320 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6913 (mp10) REVERT: a 307 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7204 (mm-30) REVERT: a 356 ASP cc_start: 0.7214 (t70) cc_final: 0.6822 (t0) REVERT: a 392 TYR cc_start: 0.7133 (m-80) cc_final: 0.6894 (m-80) outliers start: 66 outliers final: 54 residues processed: 449 average time/residue: 0.1377 time to fit residues: 92.9103 Evaluate side-chains 473 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 415 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Chi-restraints excluded: chain a residue 401 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 161 optimal weight: 0.4980 chunk 166 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 182 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS A 157 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS c 373 HIS c 408 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.170109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140376 restraints weight = 29011.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.145446 restraints weight = 15769.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.148760 restraints weight = 10383.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.150878 restraints weight = 7742.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.152557 restraints weight = 6348.009| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17877 Z= 0.196 Angle : 0.713 18.038 24306 Z= 0.343 Chirality : 0.046 0.287 2781 Planarity : 0.005 0.058 3021 Dihedral : 6.477 55.500 2973 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.61 % Allowed : 18.63 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.18), residues: 2124 helix: -1.01 (0.29), residues: 312 sheet: 0.28 (0.21), residues: 684 loop : -1.00 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 46 TYR 0.023 0.002 TYR D 50 PHE 0.019 0.002 PHE a 261 TRP 0.016 0.002 TRP a 385 HIS 0.006 0.001 HIS G 210 Details of bonding type rmsd covalent geometry : bond 0.00453 (17820) covalent geometry : angle 0.66589 (24162) SS BOND : bond 0.00532 ( 27) SS BOND : angle 1.44927 ( 54) hydrogen bonds : bond 0.04271 ( 593) hydrogen bonds : angle 6.06043 ( 1521) link_BETA1-4 : bond 0.00181 ( 4) link_BETA1-4 : angle 1.96686 ( 12) link_NAG-ASN : bond 0.00746 ( 26) link_NAG-ASN : angle 4.38104 ( 78) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 429 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 LYS cc_start: 0.6740 (tppt) cc_final: 0.6522 (mmmt) REVERT: C 154 CYS cc_start: 0.3130 (OUTLIER) cc_final: 0.2678 (p) REVERT: D 83 ASP cc_start: 0.7421 (m-30) cc_final: 0.6928 (m-30) REVERT: D 107 GLU cc_start: 0.6613 (pt0) cc_final: 0.6144 (pt0) REVERT: E 80 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5934 (pt) REVERT: E 83 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7700 (tp-100) REVERT: E 179 VAL cc_start: 0.8316 (p) cc_final: 0.7982 (m) REVERT: A 66 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6508 (tm-30) REVERT: A 68 GLN cc_start: 0.7509 (mt0) cc_final: 0.6976 (mt0) REVERT: A 133 MET cc_start: 0.7963 (tpp) cc_final: 0.7190 (tpp) REVERT: A 213 MET cc_start: 0.7171 (tmm) cc_final: 0.6775 (tmm) REVERT: H 88 ARG cc_start: 0.7251 (mmm160) cc_final: 0.6929 (mmm160) REVERT: H 211 LYS cc_start: 0.8352 (tppt) cc_final: 0.7913 (tppt) REVERT: B 87 LYS cc_start: 0.7240 (tppt) cc_final: 0.6946 (tppt) REVERT: B 133 MET cc_start: 0.7660 (tpp) cc_final: 0.6795 (tpt) REVERT: B 236 SER cc_start: 0.7538 (t) cc_final: 0.7249 (m) REVERT: F 164 SER cc_start: 0.7775 (m) cc_final: 0.6804 (t) REVERT: G 118 THR cc_start: 0.7973 (OUTLIER) cc_final: 0.7708 (p) REVERT: c 299 LYS cc_start: 0.7580 (mtmm) cc_final: 0.7283 (mtmm) REVERT: b 320 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.6948 (mp10) REVERT: a 356 ASP cc_start: 0.7228 (t70) cc_final: 0.6813 (t0) REVERT: a 392 TYR cc_start: 0.7132 (m-80) cc_final: 0.6913 (m-80) outliers start: 69 outliers final: 57 residues processed: 456 average time/residue: 0.1388 time to fit residues: 95.0888 Evaluate side-chains 488 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 427 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 336 ILE Chi-restraints excluded: chain b residue 373 HIS Chi-restraints excluded: chain b residue 383 LYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Chi-restraints excluded: chain a residue 401 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 79 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN E 102 HIS A 157 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS c 353 HIS c 373 HIS c 408 ASN a 352 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.166423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.136838 restraints weight = 28996.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.141792 restraints weight = 15853.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.145042 restraints weight = 10511.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.147195 restraints weight = 7886.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.148692 restraints weight = 6456.607| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 17877 Z= 0.292 Angle : 0.791 18.362 24306 Z= 0.388 Chirality : 0.048 0.318 2781 Planarity : 0.005 0.062 3021 Dihedral : 6.796 55.164 2973 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 4.08 % Allowed : 18.84 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.18), residues: 2124 helix: -1.33 (0.28), residues: 294 sheet: 0.09 (0.20), residues: 717 loop : -1.21 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 99 TYR 0.024 0.002 TYR D 50 PHE 0.024 0.002 PHE H 96 TRP 0.059 0.003 TRP C 226 HIS 0.010 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00670 (17820) covalent geometry : angle 0.74939 (24162) SS BOND : bond 0.00640 ( 27) SS BOND : angle 1.72335 ( 54) hydrogen bonds : bond 0.04987 ( 593) hydrogen bonds : angle 6.36187 ( 1521) link_BETA1-4 : bond 0.00309 ( 4) link_BETA1-4 : angle 2.20239 ( 12) link_NAG-ASN : bond 0.00742 ( 26) link_NAG-ASN : angle 4.24046 ( 78) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 449 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7725 (mmm) cc_final: 0.6676 (tpt) REVERT: C 154 CYS cc_start: 0.3122 (OUTLIER) cc_final: 0.2630 (p) REVERT: D 83 ASP cc_start: 0.7459 (m-30) cc_final: 0.7014 (m-30) REVERT: D 107 GLU cc_start: 0.6616 (pt0) cc_final: 0.6155 (pt0) REVERT: E 64 VAL cc_start: 0.8520 (m) cc_final: 0.8265 (t) REVERT: E 80 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.5980 (pt) REVERT: E 83 GLN cc_start: 0.7980 (tp-100) cc_final: 0.7654 (tp-100) REVERT: E 179 VAL cc_start: 0.8316 (p) cc_final: 0.7975 (m) REVERT: A 66 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6415 (tm-30) REVERT: A 68 GLN cc_start: 0.7544 (mt0) cc_final: 0.6997 (mt0) REVERT: A 213 MET cc_start: 0.7175 (tmm) cc_final: 0.6794 (tmm) REVERT: H 88 ARG cc_start: 0.7232 (mmm160) cc_final: 0.6868 (mmm160) REVERT: H 118 THR cc_start: 0.7555 (p) cc_final: 0.7351 (p) REVERT: H 211 LYS cc_start: 0.8378 (tppt) cc_final: 0.7917 (tppt) REVERT: B 87 LYS cc_start: 0.7376 (tppt) cc_final: 0.7103 (tppt) REVERT: B 133 MET cc_start: 0.7802 (tpp) cc_final: 0.7083 (tpt) REVERT: B 236 SER cc_start: 0.7705 (t) cc_final: 0.7305 (m) REVERT: F 164 SER cc_start: 0.7908 (m) cc_final: 0.6885 (t) REVERT: F 209 LYS cc_start: 0.7433 (mmtt) cc_final: 0.7233 (mmtm) REVERT: G 118 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7775 (p) REVERT: c 299 LYS cc_start: 0.7603 (mtmm) cc_final: 0.7296 (mtmm) REVERT: b 320 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6956 (mp10) REVERT: a 356 ASP cc_start: 0.7239 (t70) cc_final: 0.6857 (t0) outliers start: 78 outliers final: 65 residues processed: 478 average time/residue: 0.1313 time to fit residues: 95.1285 Evaluate side-chains 516 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 447 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 336 ILE Chi-restraints excluded: chain b residue 373 HIS Chi-restraints excluded: chain b residue 383 LYS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain b residue 388 SER Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Chi-restraints excluded: chain a residue 401 ASP Chi-restraints excluded: chain a residue 409 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 122 optimal weight: 0.9990 chunk 131 optimal weight: 0.0770 chunk 17 optimal weight: 0.8980 chunk 81 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 111 optimal weight: 0.1980 chunk 166 optimal weight: 0.0870 chunk 12 optimal weight: 0.0870 chunk 103 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 overall best weight: 0.1494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS A 157 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 102 HIS ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS G 3 GLN G 102 HIS c 353 HIS c 373 HIS c 408 ASN a 352 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.172002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.143158 restraints weight = 29187.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.147956 restraints weight = 16374.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.151106 restraints weight = 10995.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.153312 restraints weight = 8330.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.154728 restraints weight = 6788.690| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17877 Z= 0.118 Angle : 0.717 17.791 24306 Z= 0.338 Chirality : 0.045 0.278 2781 Planarity : 0.005 0.057 3021 Dihedral : 6.246 55.662 2973 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.93 % Allowed : 20.72 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.19), residues: 2124 helix: -0.80 (0.31), residues: 294 sheet: 0.25 (0.21), residues: 687 loop : -0.97 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 13 TYR 0.025 0.001 TYR D 50 PHE 0.018 0.001 PHE a 261 TRP 0.048 0.001 TRP C 226 HIS 0.006 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00263 (17820) covalent geometry : angle 0.67581 (24162) SS BOND : bond 0.00376 ( 27) SS BOND : angle 1.14748 ( 54) hydrogen bonds : bond 0.03680 ( 593) hydrogen bonds : angle 5.96397 ( 1521) link_BETA1-4 : bond 0.00508 ( 4) link_BETA1-4 : angle 1.80868 ( 12) link_NAG-ASN : bond 0.00862 ( 26) link_NAG-ASN : angle 4.17749 ( 78) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 432 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7459 (mmm) cc_final: 0.6842 (tpt) REVERT: C 154 CYS cc_start: 0.3083 (OUTLIER) cc_final: 0.2616 (p) REVERT: C 213 MET cc_start: 0.7606 (pmm) cc_final: 0.6955 (pmm) REVERT: C 222 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6955 (mm110) REVERT: D 83 ASP cc_start: 0.7412 (m-30) cc_final: 0.7076 (m-30) REVERT: D 107 GLU cc_start: 0.6485 (pt0) cc_final: 0.6044 (pt0) REVERT: E 83 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7632 (tp-100) REVERT: E 111 ASP cc_start: 0.6177 (p0) cc_final: 0.5955 (p0) REVERT: A 66 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6557 (tm-30) REVERT: A 68 GLN cc_start: 0.7509 (mt0) cc_final: 0.6991 (mt0) REVERT: A 133 MET cc_start: 0.7730 (tpp) cc_final: 0.6901 (tpp) REVERT: A 213 MET cc_start: 0.7053 (tmm) cc_final: 0.6677 (tmm) REVERT: H 88 ARG cc_start: 0.7095 (mmm160) cc_final: 0.6842 (mmm160) REVERT: H 211 LYS cc_start: 0.8276 (tppt) cc_final: 0.7866 (tppt) REVERT: B 236 SER cc_start: 0.7643 (t) cc_final: 0.7322 (m) REVERT: F 164 SER cc_start: 0.7749 (m) cc_final: 0.7139 (t) REVERT: G 118 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7620 (p) REVERT: G 152 VAL cc_start: 0.8772 (m) cc_final: 0.8445 (p) REVERT: c 299 LYS cc_start: 0.7570 (mtmm) cc_final: 0.7302 (mtmm) REVERT: b 307 GLU cc_start: 0.7920 (tp30) cc_final: 0.7671 (tp30) REVERT: b 320 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.6960 (mp10) REVERT: a 356 ASP cc_start: 0.7207 (t70) cc_final: 0.6919 (t70) REVERT: a 392 TYR cc_start: 0.7076 (m-80) cc_final: 0.6853 (m-80) outliers start: 56 outliers final: 45 residues processed: 453 average time/residue: 0.1363 time to fit residues: 93.6994 Evaluate side-chains 469 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 420 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 211 LYS Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain a residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 146 optimal weight: 0.0040 chunk 83 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 94 optimal weight: 0.3980 chunk 4 optimal weight: 0.1980 chunk 162 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS A 157 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS c 353 HIS c 373 HIS c 408 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.170804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142180 restraints weight = 28862.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.146909 restraints weight = 16213.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.150063 restraints weight = 10907.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.152182 restraints weight = 8232.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.153646 restraints weight = 6735.670| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17877 Z= 0.158 Angle : 0.727 17.748 24306 Z= 0.345 Chirality : 0.045 0.272 2781 Planarity : 0.005 0.061 3021 Dihedral : 6.288 55.590 2973 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.83 % Allowed : 21.30 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.19), residues: 2124 helix: -0.78 (0.31), residues: 294 sheet: 0.30 (0.21), residues: 681 loop : -0.98 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 13 TYR 0.022 0.001 TYR D 50 PHE 0.017 0.001 PHE a 261 TRP 0.043 0.002 TRP C 226 HIS 0.007 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00367 (17820) covalent geometry : angle 0.68648 (24162) SS BOND : bond 0.00465 ( 27) SS BOND : angle 1.43782 ( 54) hydrogen bonds : bond 0.03879 ( 593) hydrogen bonds : angle 5.94853 ( 1521) link_BETA1-4 : bond 0.00320 ( 4) link_BETA1-4 : angle 1.92381 ( 12) link_NAG-ASN : bond 0.00749 ( 26) link_NAG-ASN : angle 4.09123 ( 78) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 421 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 MET cc_start: 0.7466 (mmm) cc_final: 0.6361 (tpt) REVERT: C 154 CYS cc_start: 0.3094 (OUTLIER) cc_final: 0.2592 (p) REVERT: C 213 MET cc_start: 0.7569 (pmm) cc_final: 0.6935 (pmm) REVERT: D 83 ASP cc_start: 0.7431 (m-30) cc_final: 0.7101 (m-30) REVERT: D 107 GLU cc_start: 0.6438 (pt0) cc_final: 0.6019 (pt0) REVERT: E 71 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.7623 (t) REVERT: E 83 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7613 (tp-100) REVERT: A 66 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6565 (tm-30) REVERT: A 68 GLN cc_start: 0.7557 (mt0) cc_final: 0.7053 (mt0) REVERT: A 133 MET cc_start: 0.7768 (tpp) cc_final: 0.7012 (tpp) REVERT: A 213 MET cc_start: 0.7050 (tmm) cc_final: 0.6667 (tmm) REVERT: H 88 ARG cc_start: 0.7069 (mmm160) cc_final: 0.6828 (mmm160) REVERT: H 211 LYS cc_start: 0.8298 (tppt) cc_final: 0.7874 (tppt) REVERT: B 236 SER cc_start: 0.7685 (t) cc_final: 0.7370 (m) REVERT: F 164 SER cc_start: 0.7833 (m) cc_final: 0.6879 (t) REVERT: G 118 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7568 (p) REVERT: G 152 VAL cc_start: 0.8594 (m) cc_final: 0.8278 (p) REVERT: c 299 LYS cc_start: 0.7560 (mtmm) cc_final: 0.7300 (mtmm) REVERT: b 320 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7038 (mp10) REVERT: a 356 ASP cc_start: 0.7230 (t70) cc_final: 0.6872 (t0) REVERT: a 392 TYR cc_start: 0.7076 (m-80) cc_final: 0.6852 (m-80) outliers start: 54 outliers final: 48 residues processed: 443 average time/residue: 0.1269 time to fit residues: 85.2566 Evaluate side-chains 472 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 420 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 211 LYS Chi-restraints excluded: chain c residue 283 MET Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain b residue 320 GLN Chi-restraints excluded: chain b residue 336 ILE Chi-restraints excluded: chain b residue 373 HIS Chi-restraints excluded: chain b residue 387 ILE Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain a residue 388 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 58 optimal weight: 0.4980 chunk 139 optimal weight: 0.0770 chunk 135 optimal weight: 0.9990 chunk 20 optimal weight: 0.0270 chunk 74 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 128 optimal weight: 0.0470 chunk 138 optimal weight: 0.9990 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS G 102 HIS c 353 HIS c 373 HIS c 408 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.171783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.143084 restraints weight = 29140.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.147867 restraints weight = 16319.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.150998 restraints weight = 10951.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.153191 restraints weight = 8284.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.154578 restraints weight = 6747.308| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17877 Z= 0.133 Angle : 0.713 17.654 24306 Z= 0.337 Chirality : 0.045 0.266 2781 Planarity : 0.005 0.062 3021 Dihedral : 6.216 55.635 2973 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.04 % Allowed : 21.09 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.19), residues: 2124 helix: -0.69 (0.31), residues: 294 sheet: 0.32 (0.21), residues: 681 loop : -0.95 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 13 TYR 0.023 0.001 TYR D 50 PHE 0.017 0.001 PHE a 261 TRP 0.040 0.002 TRP C 226 HIS 0.014 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00308 (17820) covalent geometry : angle 0.67355 (24162) SS BOND : bond 0.00415 ( 27) SS BOND : angle 1.32634 ( 54) hydrogen bonds : bond 0.03737 ( 593) hydrogen bonds : angle 5.89901 ( 1521) link_BETA1-4 : bond 0.00399 ( 4) link_BETA1-4 : angle 1.89806 ( 12) link_NAG-ASN : bond 0.00776 ( 26) link_NAG-ASN : angle 4.02138 ( 78) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3485.54 seconds wall clock time: 61 minutes 1.90 seconds (3661.90 seconds total)